Dependancies and installation
Get the pipeline
$ git clone https://forgemia.inra.fr/umr-gdec/magatt.git
Dependencies - Conda
We recommend to build the environment using conda (developped with miniconda 3, conda 4.9.2 ) with the file environment.yml:
$ conda env create -f environment.yml -n magatt
Once created, you can activate the environment with:
$ conda activate magatt
All the dependancies installed in the conda env are listed below.
Snakemake : >=5.5.2
Python: 3.5
Biopython: 1.68
numpy: 1.15
pandas: 0.23
pysam: 0.15
Bedtools: 2.27
Blat: 36
Exonerate (fastavalidcds): 2.4.0
GenomeTools: 1.5.9
gffread: 0.9.11
GMAP: 2018-05-11
NCBI-blast (BLAST+): 2.6
Samtools: 1.9
BWA: 0.7